We report the results of a study focusing on the influence of crystallization kinetics and flow behavior on structural inhomogeneities in 3D-printed parts made from polyamide 12 (PA12) and poly(lactic acid) (PLA) by dynamic mechanical analysis (DMA), differential scanning calorimetry (DSC), fast scanning calorimetry (FSC), and wide-angle X-ray diffraction (WAXD). Temperature-dependent WAXD measurements on the neat PLA filament reveal that PLA forms a single orthorhombic α phase during slow cooling and subsequent 2nd heating. The PA12 filament shows a well pronounced polymorphism with a reversible solid-solid phase transition between the (pseudo)hexagonal γ phase near room temperature and the monoclinic α' phase above the Brill transition temperature TB = 140 °C. The influence of the print bed temperature Tb on structure formation, polymorphic state, and degree of crystallinity χc of the 3D-printed parts is investigated by height and depth-dependent WAXD scans and compared with that of 3D-printed single layers, used as a reference. It is found that the heat transferred from successive layers has a strong influence on the polymorphic state of PA12 since a superimposed mixture of γ and α phases is present in the 3D-printed parts. In the case of PLA, a single α phase is formed. The print bed temperature has, in comparison to PA12, a major influence on the degree of crystallinity χc and thus the homogeneity of the 3D-printed parts, especially close to the print bed. By comparing the obtained results from WAXD, DMA, DSC, and FSC measurements with relevant printing times, guidelines for 3D-printed parts with a homogeneous structure are derived.